These are really good questions and I am wiling to be that the Project gamed through these and many more many times, using both early AI and live role players.
This is one of the deals Prime Base might well have been designed and built to handle. Being outside the issue they may be more objective, they may also have more and better data to make decisions.
Here is how I see it going down. There is a local or regional incident. There is some confusion over what local resource will be in charge. Prime Base decides and sends out the chains of command. In certain circumstances Prime Base may start issuing orders. Like yep, the lab has to be saved and if it costs a few MARS folks the effort is worth it. Conversely if a MARS group has a chance to put paid to a big bad but needs some extra muscle, that is why everyone in the Project has combat training and a weapon. Yes the harvest might be delayed but the brains at Prime have determined the effort is again worth the downside.
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